Efficiency estimation is to measure how efficient the decision making units are. The methodologies probably has been dominated by Stochastic frontier analysis (SFA, for parametric analysis) and Data envelopment analysis (for non-parametric analysis). For SFA, it is a branch of micro-economics and therefore you cannot avoid using some theories from micro-economics when measuring the efficiency. If you want to have relevant backgrounds regarding SFA, see my another post. In this article, I will try to recommend a reference list for efficiency estimation. This list will be appropriate for any researches regardless your research field.

Basic concepts
Performance Benchmarking_Measuring and Managing Performance
Introduction to Econometric Production Analysis with R
Benchmarking with DEA, SFA, and R

SFA
A Practitioner's Guide to Stochastic Frontier Analysis Using Stata

DEA
Data Envelopment Analysis: Modeling Operational Processes And Measuring Productivity 

This article will continuously be updated and I welcome anyone of you to post your experience here.